Zinc in PDB 8hxw: Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Heptylthiazole-4-Carboxylic Acid

The structure of Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Heptylthiazole-4-Carboxylic Acid, PDB code: 8hxw was solved by Y.-H.Yan, K.-R.Zhu, G.-B.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.81 / 2.39
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.71, 90.221, 125.904, 90, 90, 90
R / Rfree (%)	16.3 / 25

The binding sites of Zinc atom in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Heptylthiazole-4-Carboxylic Acid (pdb code 8hxw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Heptylthiazole-4-Carboxylic Acid, PDB code: 8hxw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Heptylthiazole-4-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Heptylthiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:44.0 occ:1.00 O A:HOH427 1.6 53.0 1.0 NE2 A:HIS179 1.9 44.5 1.0 ND1 A:HIS116 2.0 45.2 1.0 NE2 A:HIS114 2.1 42.0 1.0 CD2 A:HIS179 2.8 39.1 1.0 CE1 A:HIS116 2.9 45.5 1.0 CE1 A:HIS114 3.0 38.3 1.0 CE1 A:HIS179 3.0 41.9 1.0 CG A:HIS116 3.0 47.3 1.0 CD2 A:HIS114 3.1 41.8 1.0 CB A:HIS116 3.4 38.1 1.0 ZN A:ZN302 3.6 57.1 1.0 OD1 A:ASP118 3.9 37.3 1.0 CG A:HIS179 4.0 43.5 1.0 ND1 A:HIS179 4.0 38.0 1.0 ND1 A:HIS114 4.1 34.7 1.0 NE2 A:HIS116 4.1 45.0 1.0 SG A:CYS198 4.1 40.7 1.0 CD2 A:HIS116 4.1 42.9 1.0 CG A:HIS114 4.1 39.5 1.0 CB A:CYS198 4.2 42.7 1.0 O07 A:5ZR303 4.3 53.7 1.0 OD2 A:ASP118 4.4 46.3 1.0 CG A:ASP118 4.6 43.5 1.0 CA A:HIS116 4.8 41.6 1.0 N03 A:5ZR303 4.9 48.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Heptylthiazole-4-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Heptylthiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:57.1 occ:1.00 OD2 A:ASP118 2.1 46.3 1.0 NE2 A:HIS240 2.3 53.0 1.0 O07 A:5ZR303 2.3 53.7 1.0 N03 A:5ZR303 2.3 48.3 1.0 SG A:CYS198 2.5 40.7 1.0 O A:HOH427 2.6 53.0 1.0 CE1 A:HIS240 3.0 48.0 1.0 C04 A:5ZR303 3.1 60.6 1.0 C05 A:5ZR303 3.1 55.0 1.0 CG A:ASP118 3.2 43.5 1.0 C02 A:5ZR303 3.4 46.0 1.0 CD2 A:HIS240 3.4 52.6 1.0 OD1 A:ASP118 3.6 37.3 1.0 ZN A:ZN301 3.6 44.0 1.0 CB A:CYS198 3.7 42.7 1.0 N01 A:5ZR303 3.8 44.6 1.0 NH2 A:ARG119 4.0 41.4 1.0 ND1 A:HIS240 4.2 43.1 1.0 NE2 A:HIS179 4.3 44.5 1.0 O06 A:5ZR303 4.3 54.5 1.0 CE1 A:HIS179 4.3 41.9 1.0 C08 A:5ZR303 4.4 55.5 1.0 NE A:ARG119 4.4 39.4 1.0 CB A:ASP118 4.4 39.8 1.0 CG A:HIS240 4.4 46.2 1.0 CE1 A:HIS114 4.6 38.3 1.0 NE2 A:HIS114 4.7 42.0 1.0 CZ A:ARG119 4.7 40.3 1.0 S16 A:5ZR303 4.7 61.4 1.0 CA A:CYS198 4.9 44.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Heptylthiazole-4-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Heptylthiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:39.2 occ:1.00 ND1 B:HIS116 1.9 38.5 1.0 NE2 B:HIS179 2.0 43.6 1.0 NE2 B:HIS114 2.1 41.4 1.0 O B:HOH406 2.4 45.6 1.0 CE1 B:HIS116 2.8 37.6 1.0 CE1 B:HIS179 2.9 40.2 1.0 CD2 B:HIS179 3.0 41.1 1.0 CE1 B:HIS114 3.0 42.3 1.0 CG B:HIS116 3.0 37.9 1.0 CD2 B:HIS114 3.2 41.0 1.0 CB B:HIS116 3.5 39.2 1.0 ZN B:ZN302 3.6 52.7 1.0 NE2 B:HIS116 4.0 35.7 1.0 OD1 B:ASP118 4.0 31.4 1.0 ND1 B:HIS179 4.0 37.2 1.0 CG B:HIS179 4.1 41.4 1.0 CD2 B:HIS116 4.1 34.5 1.0 SG B:CYS198 4.1 44.9 1.0 ND1 B:HIS114 4.2 39.5 1.0 CB B:CYS198 4.3 38.4 1.0 CG B:HIS114 4.3 41.9 1.0 O07 B:5ZR303 4.4 52.9 1.0 OD2 B:ASP118 4.7 38.4 1.0 CG B:ASP118 4.8 35.6 1.0 CA B:HIS116 4.9 38.6 1.0 N03 B:5ZR303 4.9 41.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Heptylthiazole-4-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of B1 Vim-2 Mbl in Complex with 2-Amino-5- Heptylthiazole-4-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:52.7 occ:1.00 O B:HOH406 1.7 45.6 1.0 NE2 B:HIS240 2.2 43.6 1.0 OD2 B:ASP118 2.2 38.4 1.0 O07 B:5ZR303 2.4 52.9 1.0 SG B:CYS198 2.5 44.9 1.0 N03 B:5ZR303 2.6 41.9 1.0 CE1 B:HIS240 2.9 41.0 1.0 CG B:ASP118 3.2 35.6 1.0 C05 B:5ZR303 3.3 47.0 1.0 C04 B:5ZR303 3.4 52.7 1.0 CD2 B:HIS240 3.4 42.5 1.0 OD1 B:ASP118 3.5 31.4 1.0 C02 B:5ZR303 3.5 40.3 1.0 ZN B:ZN301 3.6 39.2 1.0 CB B:CYS198 3.7 38.4 1.0 N01 B:5ZR303 3.8 36.6 1.0 NH2 B:ARG119 4.0 37.9 1.0 ND1 B:HIS240 4.1 40.1 1.0 NE2 B:HIS179 4.4 43.6 1.0 CG B:HIS240 4.4 42.0 1.0 CE1 B:HIS179 4.4 40.2 1.0 O06 B:5ZR303 4.4 55.7 1.0 NE B:ARG119 4.5 29.1 1.0 CB B:ASP118 4.6 32.9 1.0 CE1 B:HIS114 4.6 42.3 1.0 C08 B:5ZR303 4.7 57.4 1.0 CZ B:ARG119 4.7 33.1 1.0 NE2 B:HIS114 4.7 41.4 1.0 CA B:CYS198 4.9 48.2 1.0 S16 B:5ZR303 5.0 52.3 1.0

Y.H.Yan, T.T.Zhang, R.Li, S.Y.Wang, L.L.Wei, X.Y.Wang, K.R.Zhu, S.R.Li, G.Q.Liang, Z.B.Yang, L.L.Yang, S.Qin, G.B.Li. Discovery of 2-Aminothiazole-4-Carboxylic Acids As Broad-Spectrum Metallo-Beta-Lactamase Inhibitors By Mimicking Carbapenem Hydrolysate Binding. J.Med.Chem. V. 66 13746 2023.
ISSN: ISSN 0022-2623
PubMed: 37791640
DOI: 10.1021/ACS.JMEDCHEM.3C01189